Contacts of the helix formed by residues 216 - 228 (chain A) in PDB entry 2D7I
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with GLY 216 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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185A ASP* 2.8 20.1 + - - -
214A ARG* 3.8 2.2 - - - +
215A GLU* 1.3 74.0 - - - +
217A LEU* 1.3 55.5 + - - -
218A ILE 3.3 2.6 + - - -
219A ARG 3.5 0.3 + - - -
220A THR* 2.5 43.1 + - - -
340A GLU 3.6 11.4 - - - -
341A ILE* 4.0 9.9 - - - -
705A UDP 3.5 9.6 - - - -
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Residues in contact with LEU 217 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A PRO* 5.2 0.7 - - + -
216A GLY* 1.3 70.6 - - - -
218A ILE* 1.3 73.2 + - + +
220A THR* 4.1 1.6 - - - -
221A ARG* 2.8 70.2 + - + +
341A ILE 3.2 25.8 + - - +
342A TRP* 3.5 20.4 - - + -
345A GLU* 3.8 9.4 - - - +
702A NGA 3.4 20.4 - - - +
705A UDP 3.3 51.5 + - + +
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Residues in contact with ILE 218 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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216A GLY 3.3 0.2 - - - -
217A LEU* 1.3 96.1 - - + +
219A ARG* 1.3 67.5 + - + +
221A ARG* 3.0 5.6 + - - +
222A MET* 3.0 22.6 + - + +
335A TYR* 3.5 35.3 - - + -
336A ASP 3.9 16.4 - - - +
337A PRO* 5.3 0.2 - - + -
339A LEU* 3.7 23.3 - - + +
340A GLU 3.5 20.0 - - - +
341A ILE 3.7 9.4 - - - +
342A TRP* 4.1 9.2 - - - +
343A GLY 4.7 0.9 - - - +
345A GLU* 3.1 26.2 - - + -
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Residues in contact with ARG 219 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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213A LYS* 5.3 0.4 - - - +
214A ARG 4.3 3.4 + - - -
215A GLU* 2.7 75.7 + - + +
216A GLY 3.5 2.4 + - - -
218A ILE* 1.3 76.9 - - + +
220A THR* 1.3 61.1 + - - +
222A MET* 3.0 13.0 + - + +
223A LEU* 2.8 27.9 + - - +
337A PRO* 3.0 38.7 + - + +
339A LEU 3.8 7.7 + - - +
340A GLU* 3.1 41.8 + - - +
341A ILE* 5.7 0.6 - - - +
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Residues in contact with THR 220 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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152A PRO* 3.7 17.9 - - + -
183A VAL* 3.4 38.1 - - + +
185A ASP* 3.1 35.3 + - + -
211A THR* 4.4 4.5 - - + +
215A GLU* 3.8 5.9 - - - +
216A GLY 2.5 31.9 + - - -
217A LEU* 3.7 6.7 - - - -
219A ARG* 1.3 72.3 - - - +
221A ARG* 1.3 61.6 + - - +
223A LEU* 3.4 4.9 + - - +
224A GLY 3.3 15.4 + - - -
705A UDP 4.1 1.1 - - - +
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Residues in contact with ARG 221 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
150A ILE* 4.4 4.9 - - - +
152A PRO* 3.7 25.5 - - + +
217A LEU* 2.8 37.4 + - + +
218A ILE 3.5 4.9 - - - +
220A THR* 1.3 77.9 - - - +
222A MET* 1.3 57.4 + - - +
224A GLY* 3.3 2.1 + - - -
225A ALA* 3.0 26.7 + - - +
235A PHE* 3.3 41.6 - - + +
236A LEU 5.8 0.4 - - - -
237A ASP* 3.8 13.1 + - - -
319A GLY 3.1 19.1 + - - -
320A GLY* 3.6 23.8 + - - -
322A PHE* 5.0 1.6 - - - -
329A PHE* 6.3 0.2 - - - -
335A TYR* 3.3 26.4 + - + -
345A GLU* 2.7 30.5 + - - -
702A NGA 3.4 7.7 + - - -
705A UDP 4.9 0.8 - - - -
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Residues in contact with MET 222 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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218A ILE* 3.0 19.2 + - + +
219A ARG* 3.0 19.4 + - + +
221A ARG* 1.3 75.5 - - - +
223A LEU* 1.3 67.1 + - - +
225A ALA* 3.1 5.3 + - - +
226A SER* 2.8 25.7 + - - -
329A PHE* 4.3 3.6 - - - -
330A TRP* 4.0 28.6 - - + -
333A GLY 4.1 6.5 - - - +
334A GLY* 4.2 3.1 - - - -
335A TYR* 3.0 58.8 - - + +
337A PRO* 4.9 10.5 - - + -
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Residues in contact with LEU 223 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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183A VAL* 3.9 11.0 - - + -
209A LEU* 3.6 27.8 - - + -
210A ARG 4.4 3.1 - - - +
211A THR* 3.5 37.2 - - + +
219A ARG 2.8 12.8 + - - +
220A THR* 3.6 9.6 - - - +
221A ARG 3.3 0.2 - - - -
222A MET* 1.3 74.8 - - - +
224A GLY* 1.3 64.5 + - - +
226A SER* 2.7 30.2 + - - +
227A VAL* 3.5 10.4 + - + +
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Residues in contact with GLY 224 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ILE* 3.8 21.5 - - - +
181A VAL* 5.1 4.8 - - - +
183A VAL* 3.9 21.7 - - - +
209A LEU* 4.6 6.7 - - - -
220A THR 3.3 5.1 + - - -
221A ARG 3.3 7.0 + - - -
222A MET 3.2 0.4 - - - -
223A LEU* 1.3 79.5 - - - +
225A ALA* 1.3 60.5 + - - +
227A VAL* 3.4 3.6 + - - +
228A ALA* 3.2 18.0 + - - +
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Residues in contact with ALA 225 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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150A ILE* 4.3 4.0 - - - +
221A ARG 3.0 17.2 + - - +
222A MET* 3.1 3.3 + - - +
224A GLY* 1.3 75.9 - - - +
226A SER* 1.3 61.0 + - - +
227A VAL 3.1 1.3 + - - -
228A ALA* 3.5 14.6 + - - +
233A ILE* 3.8 24.2 - - + +
235A PHE* 4.2 5.6 - - + -
326A ARG* 4.5 3.8 + - - -
329A PHE* 3.8 14.4 - - + -
330A TRP* 3.4 30.6 + - + -
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Residues in contact with SER 226 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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222A MET 2.8 13.0 + - - -
223A LEU* 2.7 28.0 + - - +
225A ALA* 1.3 75.5 - - - +
227A VAL* 1.3 65.6 + - - +
228A ALA 5.2 0.2 - - - -
326A ARG* 6.3 0.7 - - - -
330A TRP* 3.4 16.4 - - - +
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Residues in contact with VAL 227 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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179A GLU* 4.4 0.7 - - - +
181A VAL* 6.0 3.4 - - + -
207A ARG* 2.9 41.3 - - - +
209A LEU* 4.3 17.9 - - + -
223A LEU* 4.0 9.6 - - + +
224A GLY 3.4 6.5 + - - +
225A ALA 3.1 0.2 - - - -
226A SER* 1.3 90.8 + - - +
228A ALA* 1.3 70.2 + - - +
229A THR* 3.4 13.6 + - + +
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Residues in contact with ALA 228 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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148A SER* 3.5 23.3 - - - -
150A ILE* 4.3 4.5 - - + -
179A GLU* 3.6 7.9 - - - -
181A VAL* 5.8 1.6 - - - -
224A GLY 3.2 13.1 + - - +
225A ALA 3.5 13.1 + - - +
226A SER 5.2 0.3 - - - -
227A VAL* 1.3 80.3 - - - +
229A THR* 1.3 59.8 + - - +
230A GLY 3.6 0.2 - - - -
233A ILE* 4.2 10.1 - - + -
326A ARG* 3.3 34.3 + - - -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il